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New insights into oocyte cytoplasmic lattice-associated proteins. 对卵母细胞胞质晶格相关蛋白的新认识。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2024-10-01 Epub Date: 2024-07-01 DOI: 10.1016/j.tig.2024.06.002
Carlo Giaccari, Francesco Cecere, Lucia Argenziano, Angela Pagano, Andrea Riccio
{"title":"New insights into oocyte cytoplasmic lattice-associated proteins.","authors":"Carlo Giaccari, Francesco Cecere, Lucia Argenziano, Angela Pagano, Andrea Riccio","doi":"10.1016/j.tig.2024.06.002","DOIUrl":"10.1016/j.tig.2024.06.002","url":null,"abstract":"<p><p>Oocyte maturation and preimplantation embryo development are critical to successful pregnancy outcomes and the correct establishment and maintenance of genomic imprinting. Thanks to novel technologies and omics studies in human patients and mouse models, the importance of the proteins associated with the cytoplasmic lattices (CPLs), highly abundant structures found in the cytoplasm of mammalian oocytes and preimplantation embryos, in the maternal to zygotic transition is becoming increasingly evident. This review highlights the recent discoveries on the role of these proteins in protein storage and other oocyte cytoplasmic processes, epigenetic reprogramming, and zygotic genome activation (ZGA). A better comprehension of these events may significantly improve clinical diagnosis and pave the way for targeted interventions aiming to correct or mitigate female fertility issues and genomic imprinting disorders.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"880-890"},"PeriodicalIF":13.6,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141494289","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Artificial intelligence in plant breeding. 人工智能在植物育种中的应用。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2024-10-01 Epub Date: 2024-08-07 DOI: 10.1016/j.tig.2024.07.001
Muhammad Amjad Farooq, Shang Gao, Muhammad Adeel Hassan, Zhangping Huang, Awais Rasheed, Sarah Hearne, Boddupalli Prasanna, Xinhai Li, Huihui Li
{"title":"Artificial intelligence in plant breeding.","authors":"Muhammad Amjad Farooq, Shang Gao, Muhammad Adeel Hassan, Zhangping Huang, Awais Rasheed, Sarah Hearne, Boddupalli Prasanna, Xinhai Li, Huihui Li","doi":"10.1016/j.tig.2024.07.001","DOIUrl":"10.1016/j.tig.2024.07.001","url":null,"abstract":"<p><p>Harnessing cutting-edge technologies to enhance crop productivity is a pivotal goal in modern plant breeding. Artificial intelligence (AI) is renowned for its prowess in big data analysis and pattern recognition, and is revolutionizing numerous scientific domains including plant breeding. We explore the wider potential of AI tools in various facets of breeding, including data collection, unlocking genetic diversity within genebanks, and bridging the genotype-phenotype gap to facilitate crop breeding. This will enable the development of crop cultivars tailored to the projected future environments. Moreover, AI tools also hold promise for refining crop traits by improving the precision of gene-editing systems and predicting the potential effects of gene variants on plant phenotypes. Leveraging AI-enabled precision breeding can augment the efficiency of breeding programs and holds promise for optimizing cropping systems at the grassroots level. This entails identifying optimal inter-cropping and crop-rotation models to enhance agricultural sustainability and productivity in the field.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"891-908"},"PeriodicalIF":13.6,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141908320","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
i-Motif DNA: identification, formation, and cellular functions. i-Motif DNA：识别、形成和细胞功能。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2024-10-01 Epub Date: 2024-06-19 DOI: 10.1016/j.tig.2024.05.011
Shentong Tao, Yonghang Run, David Monchaud, Wenli Zhang
{"title":"i-Motif DNA: identification, formation, and cellular functions.","authors":"Shentong Tao, Yonghang Run, David Monchaud, Wenli Zhang","doi":"10.1016/j.tig.2024.05.011","DOIUrl":"10.1016/j.tig.2024.05.011","url":null,"abstract":"<p><p>An i-motif (iM) is a four-stranded (quadruplex) DNA structure that folds from cytosine (C)-rich sequences. iMs can fold under many different conditions in vitro, which paves the way for their formation in living cells. iMs are thought to play key roles in various DNA transactions, notably in the regulation of genome stability, gene transcription, mRNA translation, DNA replication, telomere and centromere functions, and human diseases. We summarize the different techniques used to assess the folding of iMs in vitro and provide an overview of the internal and external factors that affect their formation and stability in vivo. We describe the possible biological relevance of iMs and propose directions towards their use as target in biology.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"853-867"},"PeriodicalIF":13.6,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141433317","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Unveiling contact-mediated cellular crosstalk. 揭示接触介导的细胞串扰
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2024-10-01 Epub Date: 2024-06-21 DOI: 10.1016/j.tig.2024.05.010
Hyobin Kim, Kwang-Eun Kim, Esha Madan, Patrick Martin, Rajan Gogna, Hyun-Woo Rhee, Kyoung-Jae Won
{"title":"Unveiling contact-mediated cellular crosstalk.","authors":"Hyobin Kim, Kwang-Eun Kim, Esha Madan, Patrick Martin, Rajan Gogna, Hyun-Woo Rhee, Kyoung-Jae Won","doi":"10.1016/j.tig.2024.05.010","DOIUrl":"10.1016/j.tig.2024.05.010","url":null,"abstract":"<p><p>Cell-cell interactions orchestrate complex functions in multicellular organisms, forming a regulatory network for diverse biological processes. Their disruption leads to disease states. Recent advancements - including single-cell sequencing and spatial transcriptomics, coupled with powerful bioengineering and molecular tools - have revolutionized our understanding of how cells respond to each other. Notably, spatial transcriptomics allows us to analyze gene expression changes based on cell proximity, offering a unique window into the impact of cell-cell contact. Additionally, computational approaches are being developed to decipher how cell contact governs the symphony of cellular responses. This review explores these cutting-edge approaches, providing valuable insights into deciphering the intricate cellular changes influenced by cell-cell communication.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"868-879"},"PeriodicalIF":13.6,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141437790","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
On the evolutionary developmental biology of the cell. 细胞进化发育生物学。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2024-10-01 Epub Date: 2024-07-05 DOI: 10.1016/j.tig.2024.06.003
Leslie S Babonis
{"title":"On the evolutionary developmental biology of the cell.","authors":"Leslie S Babonis","doi":"10.1016/j.tig.2024.06.003","DOIUrl":"10.1016/j.tig.2024.06.003","url":null,"abstract":"<p><p>Organisms are complex assemblages of cells, cells that produce light, shoot harpoons, and secrete glue. Therefore, identifying the mechanisms that generate novelty at the level of the individual cell is essential for understanding how multicellular life evolves. For decades, the field of evolutionary developmental biology (Evo-Devo) has been developing a framework for connecting genetic variation that arises during embryonic development to the emergence of diverse adult forms. With increasing access to new single cell 'omics technologies and an array of techniques for manipulating gene expression, we can now extend these inquiries inward to the level of the individual cell. In this opinion, I argue that applying an Evo-Devo framework to single cells makes it possible to explore the natural history of cells, where this was once only possible at the organismal level.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"822-833"},"PeriodicalIF":13.6,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141545553","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Circadian clock gene polymorphisms implicated in human pathologies. 与人类病症有关的昼夜节律钟基因多态性。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2024-10-01 Epub Date: 2024-06-12 DOI: 10.1016/j.tig.2024.05.006
Jesse R Janoski, Ignacio Aiello, Clayton W Lundberg, Carla V Finkielstein
{"title":"Circadian clock gene polymorphisms implicated in human pathologies.","authors":"Jesse R Janoski, Ignacio Aiello, Clayton W Lundberg, Carla V Finkielstein","doi":"10.1016/j.tig.2024.05.006","DOIUrl":"10.1016/j.tig.2024.05.006","url":null,"abstract":"<p><p>Circadian rhythms, ~24 h cycles of physiological and behavioral processes, can be synchronized by external signals (e.g., light) and persist even in their absence. Consequently, dysregulation of circadian rhythms adversely affects the well-being of the organism. This timekeeping system is generated and sustained by a genetically encoded endogenous mechanism composed of interlocking transcriptional/translational feedback loops that generate rhythmic expression of core clock genes. Genome-wide association studies (GWAS) and forward genetic studies show that SNPs in clock genes influence gene regulation and correlate with the risk of developing various conditions. We discuss genetic variations in core clock genes that are associated with various phenotypes, their implications for human health, and stress the need for thorough studies in this domain of circadian regulation.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"834-852"},"PeriodicalIF":13.6,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141319024","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Dosage compensation in non-model insects - progress and perspectives. 非模式昆虫的剂量补偿--进展与前景。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2024-09-27 DOI: 10.1016/j.tig.2024.08.010
Agata Izabela Kalita, Claudia Isabelle Keller Valsecchi
{"title":"Dosage compensation in non-model insects - progress and perspectives.","authors":"Agata Izabela Kalita, Claudia Isabelle Keller Valsecchi","doi":"10.1016/j.tig.2024.08.010","DOIUrl":"https://doi.org/10.1016/j.tig.2024.08.010","url":null,"abstract":"<p><p>In many multicellular eukaryotes, heteromorphic sex chromosomes are responsible for determining the sexual characteristics and reproductive functions of individuals. Sex chromosomes can cause a dosage imbalance between sexes, which in some species is re-equilibrated by dosage compensation (DC). Recent genomic advances have extended our understanding of DC mechanisms in insects beyond model organisms such as Drosophila melanogaster. We review current knowledge of insect DC, focusing on its conservation and divergence across orders, the evolutionary dynamics of neo-sex chromosomes, and the diversity of molecular mechanisms. We propose a framework to uncover DC regulators in non-model insects that relies on integrating evolutionary, genomic, and functional approaches. This comprehensive approach will facilitate a deeper understanding of the evolution and essentiality of gene regulatory mechanisms.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":""},"PeriodicalIF":13.6,"publicationDate":"2024-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142332463","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Genetic origins, regulators, and biomarkers of cellular senescence. 细胞衰老的遗传起源、调节因子和生物标志物。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2024-09-27 DOI: 10.1016/j.tig.2024.08.007
Grasiela Torres, Ivan A Salladay-Perez, Anika Dhingra, Anthony J Covarrubias
{"title":"Genetic origins, regulators, and biomarkers of cellular senescence.","authors":"Grasiela Torres, Ivan A Salladay-Perez, Anika Dhingra, Anthony J Covarrubias","doi":"10.1016/j.tig.2024.08.007","DOIUrl":"https://doi.org/10.1016/j.tig.2024.08.007","url":null,"abstract":"<p><p>This review comprehensively examines the molecular biology and genetic origins of cellular senescence. We focus on various cellular stressors and pathways leading to senescence, including recent advances in the understanding of the genetic influences driving senescence, such as telomere attrition, chemotherapy-induced DNA damage, pathogens, oncogene activation, and cellular and metabolic stress. This review also highlights the complex interplay of various signaling and metabolic pathways involved in cellular senescence and provides insights into potential therapeutic targets for aging-related diseases. Furthermore, this review outlines future research directions to deepen our understanding of senescence biology and develop effective interventions targeting senescent cells (SnCs).</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":""},"PeriodicalIF":13.6,"publicationDate":"2024-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142332464","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The complex universe of inactive PARP1. 非活性 PARP1 的复杂世界。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2024-09-20 DOI: 10.1016/j.tig.2024.08.009
Doudou Huang, Ziyi Su, Yanxia Mei, Zhengping Shao
{"title":"The complex universe of inactive PARP1.","authors":"Doudou Huang, Ziyi Su, Yanxia Mei, Zhengping Shao","doi":"10.1016/j.tig.2024.08.009","DOIUrl":"https://doi.org/10.1016/j.tig.2024.08.009","url":null,"abstract":"<p><p>Poly(ADP-ribose) polymerase 1 (PARP1) is a crucial member of the PARP family, which modifies targets through ADP-ribosylation and plays key roles in a variety of biological processes. PARP inhibitors (PARPis) hinder ADP-ribosylation and lead to the retention of PARP1 at the DNA lesion (also known as trapping), which underlies their toxicity. However, inhibitors and mutations that make PARP1 inactive do not necessarily correlate with trapping potency, challenging the current understanding of inactivation-caused trapping. Recent studies on mouse models indicate that both trapping and non-trapping inactivating mutations of PARP1 lead to embryonic lethality, suggesting the unexpected toxicity of the current inhibition strategy. The allosteric model, complicated automodification, and various biological functions of PARP1 all contribute to the complexity of PARP1 inactivation.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":""},"PeriodicalIF":13.6,"publicationDate":"2024-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142301092","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Why do mobile genetic elements transfer DNA of their hosts? 为什么流动遗传因子会转移宿主的 DNA？
IF 11.4 2区 生物学
Trends in Genetics Pub Date : 2024-09-19 DOI: 10.1016/j.tig.2024.07.008
Michiel Vos, Angus Buckling, Bram Kuijper, Adam Eyre-Walker, Cyril Bontemps, Pierre Leblond, Tatiana Dimitriu
{"title":"Why do mobile genetic elements transfer DNA of their hosts?","authors":"Michiel Vos, Angus Buckling, Bram Kuijper, Adam Eyre-Walker, Cyril Bontemps, Pierre Leblond, Tatiana Dimitriu","doi":"10.1016/j.tig.2024.07.008","DOIUrl":"https://doi.org/10.1016/j.tig.2024.07.008","url":null,"abstract":"<p>The prokaryote world is replete with mobile genetic elements (MGEs) – self-replicating entities that can move within and between their hosts. Many MGEs not only transfer their own DNA to new hosts but also transfer host DNA located elsewhere on the chromosome in the process. This could potentially lead to indirect benefits to the host when the resulting increase in chromosomal variation results in more efficient natural selection. We review the diverse ways in which MGEs promote the transfer of host DNA and explore the benefits and costs to MGEs and hosts. In many cases, MGE-mediated transfer of host DNA might not be selected for because of a sex function, but evidence of MGE domestication suggests that there may be host benefits of MGE-mediated sex.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":"6 1","pages":""},"PeriodicalIF":11.4,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142263518","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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